Inertial reference systems are able to provide measurements that are used by a vehicle to determine the vehicle's navigation solution. For example, an inertial reference system may include multiple gyroscopes and accelerometers that provide measurements that are used by a vehicle to determine the position, attitude, velocity, and heading of the vehicle. When an inertial reference system commences operation, the inertial reference system performs alignment to find its orientation (roll, pitch and heading angles) with respect to a reference axis for the system, for example the local level frame. However, vibrations during the alignment phase of the inertial reference system may negatively affect the ability of the inertial reference system to align itself in a timely manner. For example, when the vehicle is a helicopter, during the alignment phase, the helicopter is spooling up the rotor. Rotor spool up can cause a large varying vibration that can slow the convergence of the inertial reference system to a satisfactory alignment state.